shnitsel._generated_accessors

Attributes

default_mol

Classes

DataArrayAccessor
DatasetAccessor

Module Contents

default_mol

class DataArrayAccessor(obj)

Bases: shnitsel._accessors.DAManualAccessor

_methods = ['norm', 'subtract_combinations', 'keep_norming', 'pwdists', 'calc_confidence_interval',...

norm(dim='direction', keep_attrs=None)

Wrapper for shnitsel.analyze.generic.norm().

Parameters:

• dim (str)

• keep_attrs (bool | str | None)

Return type:

shnitsel.core.typedefs.DataArrayOrVar

subtract_combinations(dim, add_labels=False)

Wrapper for shnitsel.analyze.generic.subtract_combinations().

Parameters:

• dim (str)

• add_labels (bool)

Return type:

xarray.core.dataarray.DataArray

keep_norming(exclude=None)

Wrapper for shnitsel.analyze.generic.keep_norming().

Parameters:

exclude (Optional)

Return type:

xarray.core.dataarray.DataArray

pwdists(center_mean=False)

Wrapper for shnitsel.analyze.generic.pwdists().

Parameters:

center_mean (bool)

Return type:

xarray.core.dataarray.DataArray

calc_confidence_interval(confidence=0.95)

Wrapper for shnitsel.analyze.stats.calc_confidence_interval().

Parameters:

confidence (float)

Return type:

numpy.ndarray

time_grouped_confidence_interval(confidence=0.9)

Wrapper for shnitsel.analyze.stats.time_grouped_confidence_interval().

Parameters:

confidence (float)

Return type:

xarray.core.dataset.Dataset

to_xyz(comment='#', units='angstrom')

Wrapper for shnitsel.bridges.to_xyz().

Return type:

str

traj_to_xyz(units='angstrom')

Wrapper for shnitsel.bridges.traj_to_xyz().

Return type:

str

to_mol(charge=None, covFactor=1.2, to2D=True, molAtomMapNumber=None, atomNote=None, atomLabel=None)

Wrapper for shnitsel.bridges.to_mol().

Parameters:

• charge (int | None)

• covFactor (float)

• to2D (bool)

• molAtomMapNumber (Union)

• atomNote (Union)

• atomLabel (Union)

Return type:

rdkit.Chem.rdchem.Mol

smiles_map(charge=0, covFactor=1.5)

Wrapper for shnitsel.bridges.smiles_map().

Return type:

str

default_mol(to2D=True, charge=None, molAtomMapNumber=None, atomNote=None, atomLabel=None, silent_mode=False)

Wrapper for shnitsel.bridges.default_mol().

Parameters:

• to2D (bool)

• charge (int | float | None)

• molAtomMapNumber (Union)

• atomNote (Union)

• atomLabel (Union)

• silent_mode (bool)

Return type:

rdkit.Chem.rdchem.Mol

convert_energy(to, convert_from=None)

Wrapper for shnitsel.units.conversion.convert_energy().

Parameters:

• to (str)

• convert_from (str | None)

convert_force(to, convert_from=None)

Wrapper for shnitsel.units.conversion.convert_force().

Parameters:

• to (str)

• convert_from (str | None)

convert_dipole(to, convert_from=None)

Wrapper for shnitsel.units.conversion.convert_dipole().

Parameters:

• to (str)

• convert_from (str | None)

convert_length(to, convert_from=None)

Wrapper for shnitsel.units.conversion.convert_length().

Parameters:

• to (str)

• convert_from (str | None)

convert_time(to, convert_from=None)

Wrapper for shnitsel.units.conversion.convert_time().

Parameters:

• to (str)

• convert_from (str | None)

convert_nacs(to, convert_from=None)

Wrapper for shnitsel.units.conversion.convert_nacs().

Parameters:

• to (str)

• convert_from (str | None)

mdiff(dim=None)

Wrapper for shnitsel.data.multi_indices.mdiff().

Parameters:

dim (str | None)

Return type:

xarray.DataArray

flatten_levels(idx_name, levels, new_name=None, position=0, renamer=None)

Wrapper for shnitsel.data.multi_indices.flatten_levels().

Parameters:

• idx_name (str)

• levels (Sequence[str])

• new_name (str | None)

• position (int)

• renamer (Callable | None)

Return type:

shnitsel.core.typedefs.DatasetOrArray

expand_midx(midx_name, level_name, value)

Wrapper for shnitsel.data.multi_indices.expand_midx().

Parameters:

• midx_name (str)

• level_name (str)

Return type:

shnitsel.core.typedefs.DatasetOrArray

assign_levels(levels=None, **levels_kwargs)

Wrapper for shnitsel.data.multi_indices.assign_levels().

Parameters:

• levels (dict[str, numpy.typing.ArrayLike] | None)

• levels_kwargs (numpy.typing.ArrayLike)

Return type:

shnitsel.core.typedefs.DatasetOrArray

mgroupby(levels)

Wrapper for shnitsel.data.multi_indices.mgroupby().

Parameters:

levels (Sequence[str])

Return type:

xarray.core.groupby.DataArrayGroupBy | xarray.core.groupby.DatasetGroupBy

msel(**kwargs)

Wrapper for shnitsel.data.multi_indices.msel().

Return type:

shnitsel.core.typedefs.DatasetOrArray

sel_trajs(trajids_or_mask, invert=False)

Wrapper for shnitsel.data.multi_indices.sel_trajs().

Parameters:

• trajids_or_mask (Sequence[int] | Sequence[bool])

• invert (bool)

Return type:

shnitsel.core.typedefs.DatasetOrArray

stack_trajs()

Wrapper for shnitsel.data.multi_indices.stack_trajs().

Return type:

shnitsel.core.typedefs.DatasetOrArray

unstack_trajs(fill_value=shnitsel.data.multi_indices.dtype_NA)

Wrapper for shnitsel.data.multi_indices.unstack_trajs().

Return type:

shnitsel.core.typedefs.DatasetOrArray

true_upto(dim)

Wrapper for shnitsel.clean.common.true_upto().

Parameters:

dim (str)

Return type:

xarray.core.dataarray.DataArray

distance(i, j)

Wrapper for shnitsel.geo.geocalc_.distances.distance().

Parameters:

• i (int)

• j (int)

Return type:

xarray.core.dataarray.DataArray

angle(a_index, b_index, c_index, deg=False)

Wrapper for shnitsel.geo.geocalc_.angles.angle().

Parameters:

• a_index (int)

• b_index (int)

• c_index (int)

• deg (bool)

Return type:

xarray.core.dataarray.DataArray

dihedral(a_index, b_index, c_index, d_index, deg=True, full=False)

Wrapper for shnitsel.geo.geocalc_.dihedrals.dihedral().

Parameters:

• a_index (int)

• b_index (int)

• c_index (int)

• d_index (int)

• deg (Union)

• full (bool)

Return type:

xarray.core.dataarray.DataArray | tuple[xarray.core.dataarray.DataArray, xarray.core.dataarray.DataArray]

pyramidalization_angle(x_index, a_index, b_index, c_index, deg=True)

Wrapper for shnitsel.geo.geocalc_.pyramids.pyramidalization_angle().

Parameters:

• x_index (int)

• a_index (int)

• b_index (int)

• c_index (int)

• deg (Union)

Return type:

xarray.core.dataarray.DataArray | tuple[xarray.core.dataarray.DataArray, xarray.core.dataarray.DataArray]

get_bats(structure_selection=None, default_features=['bonds', 'angles', 'dihedrals'], signed=False, deg=True)

Wrapper for shnitsel.geo.geocalc.get_bats().

Parameters:

• structure_selection (Union)

• default_features (Sequence)

• signed (bool)

• deg (Union)

Return type:

xarray.core.dataarray.DataArray | shnitsel.data.tree.node.TreeNode[DataArray]

get_distances(structure_selection=None)

Wrapper for shnitsel.geo.geocalc_.distances.get_distances().

Parameters:

structure_selection (Union)

Return type:

shnitsel.data.tree.node.TreeNode[DataArray] | xarray.core.dataarray.DataArray

get_angles(structure_selection=None, deg=True, signed=True)

Wrapper for shnitsel.geo.geocalc_.angles.get_angles().

Parameters:

• structure_selection (Union)

• deg (Union)

• signed (bool)

Return type:

shnitsel.data.tree.node.TreeNode[DataArray] | xarray.core.dataarray.DataArray

get_dihedrals(structure_selection=None, deg=True, signed=True)

Wrapper for shnitsel.geo.geocalc_.dihedrals.get_dihedrals().

Parameters:

• structure_selection (Union)

• deg (Union)

• signed (bool)

Return type:

shnitsel.data.tree.node.TreeNode[DataArray] | xarray.core.dataarray.DataArray

get_pyramidalization(structure_selection=None, deg=True, signed=True)

Wrapper for shnitsel.geo.geocalc_.pyramids.get_pyramidalization().

Parameters:

• structure_selection (Union)

• deg (Union)

• signed (bool)

Return type:

shnitsel.data.tree.node.TreeNode[DataArray] | xarray.core.dataarray.DataArray

get_max_chromophor_BLA(structure_selection=None, SMARTS=None, num_double_bonds=None, allowed_chain_elements='#6,#7,#8,#15,#16', max_considered_BLA_double_bonds=50)

Wrapper for shnitsel.geo.geocalc_.bla_chromophor.get_max_chromophor_BLA().

Parameters:

• structure_selection (Union)

• SMARTS (str | None)

• num_double_bonds (int | None)

• allowed_chain_elements (str)

• max_considered_BLA_double_bonds (int)

Return type:

shnitsel.data.tree.node.TreeNode[DataArray] | xarray.core.dataarray.DataArray

kabsch(reference_or_indexers=None, **indexers_kwargs)

Wrapper for shnitsel.geo.alignment.kabsch().

Parameters:

reference_or_indexers (xarray.core.dataarray.DataArray | dict | None)

Return type:

xarray.core.dataarray.DataArray

FrameSelector(data_var=None, dim=None, xname=None, yname=None, title='', allowed_ws_origin=None, webgl=True)

Wrapper for shnitsel.vis.plot.select.FrameSelector().

TrajSelector(data_var=None, dim=None, xname=None, yname=None, title='', allowed_ws_origin=None, webgl=True)

Wrapper for shnitsel.vis.plot.select.TrajSelector().

frame3D()

Wrapper for shnitsel.vis.plot.p3mhelpers.frame3D().

frames3Dgrid()

Wrapper for shnitsel.vis.plot.p3mhelpers.frames3Dgrid().

traj3D()

Wrapper for shnitsel.vis.plot.p3mhelpers.traj3D().

trajs3Dgrid(trajids=None, loop='forward')

Wrapper for shnitsel.vis.plot.p3mhelpers.trajs3Dgrid().

Parameters:

• trajids (list[int | str] | None)

• loop (str)

traj_vmd(groupby='trajid')

Wrapper for shnitsel.vis.vmd.traj_vmd().

pca(structure_selection=None, dim=None, n_components=2, center_mean=False)

Wrapper for shnitsel.analyze.pca.pca().

Parameters:

• structure_selection (Union)

• dim (Optional)

• n_components (int)

• center_mean (bool)

Return type:

Union

lda(dim, cats, n_components=2)

Wrapper for shnitsel.analyze.lda.lda().

Parameters:

• dim (str)

• cats (str | xarray.core.dataarray.DataArray)

• n_components (int)

Return type:

xarray.core.dataarray.DataArray

pls(ydata_array, n_components=2, common_dim=None)

Wrapper for shnitsel.analyze.pls.pls().

Parameters:

• ydata_array (xarray.core.dataarray.DataArray)

• n_components (int)

• common_dim (str | None)

Return type:

xarray.core.dataset.Dataset

hops_mask_from_active_state(hop_type_selection=None, dim=None)

Wrapper for shnitsel.analyze.hops.hops_mask_from_active_state().

Parameters:

• hop_type_selection (Union)

• dim (str | None)

Return type:

xarray.core.dataarray.DataArray | shnitsel.data.tree.node.TreeNode[DataArray]

filter_data_at_hops(hop_type_selection=None)

Wrapper for shnitsel.analyze.hops.filter_data_at_hops().

Parameters:

hop_type_selection (Union)

Return type:

shnitsel.data.dataset_containers.data_series.DataSeries | xarray.core.dataarray.DataArray | shnitsel.data.tree.node.TreeNode[DataSeries] | shnitsel.data.tree.node.TreeNode[DataArray]

focus_hops(hop_types=None, window=None)

Wrapper for shnitsel.analyze.hops.focus_hops().

Parameters:

• hop_types (list[tuple[int, int]] | None)

• window (slice | None)

assign_hop_time(hop_types=None, which='last')

Wrapper for shnitsel.analyze.hops.assign_hop_time().

Parameters:

• hop_types (list[tuple[int, int]] | None)

• which (Literal)

class DatasetAccessor(obj)

Bases: shnitsel._accessors.DSManualAccessor

_methods = ['pca_and_hops', 'validate', 'get_spectra', 'get_per_state', 'get_inter_state',...

pca_and_hops(structure_selection=None, center_mean=False, n_components=2)

Wrapper for shnitsel.analyze.pca.pca_and_hops().

Parameters:

• structure_selection (Union)

• center_mean (bool)

• n_components (int)

Return type:

Union

validate()

Wrapper for shnitsel.data.helpers.validate().

Return type:

numpy.ndarray

get_spectra(state_selection=None, times=None, rel_cutoff=0.01)

Wrapper for shnitsel.analyze.spectra.get_spectra().

Parameters:

• state_selection (shnitsel.filtering.state_selection.StateSelection | None)

• times (Union)

• rel_cutoff (float)

Return type:

Union

get_per_state()

Wrapper for shnitsel.analyze.stats.get_per_state().

Return type:

xarray.core.dataset.Dataset

get_inter_state()

Wrapper for shnitsel.analyze.stats.get_inter_state().

Return type:

xarray.core.dataset.Dataset

calc_classical_populations()

Wrapper for shnitsel.analyze.populations.calc_classical_populations().

Return type:

shnitsel.analyze.populations.PopulationStatistics | shnitsel.data.tree.node.TreeNode[PopulationStatistics]

default_mol(to2D=True, charge=None, molAtomMapNumber=None, atomNote=None, atomLabel=None, silent_mode=False)

Wrapper for shnitsel.bridges.default_mol().

Parameters:

• to2D (bool)

• charge (int | float | None)

• molAtomMapNumber (Union)

• atomNote (Union)

• atomLabel (Union)

• silent_mode (bool)

Return type:

rdkit.Chem.rdchem.Mol

flatten_levels(idx_name, levels, new_name=None, position=0, renamer=None)

Wrapper for shnitsel.data.multi_indices.flatten_levels().

Parameters:

• idx_name (str)

• levels (Sequence[str])

• new_name (str | None)

• position (int)

• renamer (Callable | None)

Return type:

shnitsel.core.typedefs.DatasetOrArray

expand_midx(midx_name, level_name, value)

Wrapper for shnitsel.data.multi_indices.expand_midx().

Parameters:

• midx_name (str)

• level_name (str)

Return type:

shnitsel.core.typedefs.DatasetOrArray

assign_levels(levels=None, **levels_kwargs)

Wrapper for shnitsel.data.multi_indices.assign_levels().

Parameters:

• levels (dict[str, numpy.typing.ArrayLike] | None)

• levels_kwargs (numpy.typing.ArrayLike)

Return type:

shnitsel.core.typedefs.DatasetOrArray

mgroupby(levels)

Wrapper for shnitsel.data.multi_indices.mgroupby().

Parameters:

levels (Sequence[str])

Return type:

xarray.core.groupby.DataArrayGroupBy | xarray.core.groupby.DatasetGroupBy

msel(**kwargs)

Wrapper for shnitsel.data.multi_indices.msel().

Return type:

shnitsel.core.typedefs.DatasetOrArray

sel_trajs(trajids_or_mask, invert=False)

Wrapper for shnitsel.data.multi_indices.sel_trajs().

Parameters:

• trajids_or_mask (Sequence[int] | Sequence[bool])

• invert (bool)

Return type:

shnitsel.core.typedefs.DatasetOrArray

unstack_trajs(fill_value=shnitsel.data.multi_indices.dtype_NA)

Wrapper for shnitsel.data.multi_indices.unstack_trajs().

Return type:

shnitsel.core.typedefs.DatasetOrArray

stack_trajs()

Wrapper for shnitsel.data.multi_indices.stack_trajs().

Return type:

shnitsel.core.typedefs.DatasetOrArray

write_shnitsel_file(savepath, complevel=9)

Wrapper for shnitsel.io.shnitsel.write.write_shnitsel_file().

Parameters:

• savepath (str | os.PathLike)

• complevel (int)

calculate_energy_filtranda(energy_thresholds=None)

Wrapper for shnitsel.clean.filter_energy.calculate_energy_filtranda().

Parameters:

energy_thresholds (dict[str, float] | shnitsel.clean.filter_energy.EnergyFiltrationThresholds | None)

Return type:

xarray.core.dataarray.DataArray

filter_by_energy(filter_method='truncate', energy_thresholds=None, plot_thresholds=False, plot_populations=False)

Wrapper for shnitsel.clean.filter_energy.filter_by_energy().

Parameters:

• filter_method (Union)

• energy_thresholds (dict[str, float] | shnitsel.clean.filter_energy.EnergyFiltrationThresholds | None)

• plot_thresholds (Union)

• plot_populations (Literal)

Return type:

Optional

sanity_check(filter_method='truncate', energy_thresholds=None, geometry_thresholds=None, plot_thresholds=False, plot_populations=False, mol=None, drop_empty_trajectories=False)

Wrapper for shnitsel.clean.sanity_check().

Parameters:

• filter_method (Union)

• energy_thresholds (dict[str, float] | shnitsel.clean.filter_energy.EnergyFiltrationThresholds | None)

• geometry_thresholds (dict[str, float] | shnitsel.clean.filter_geo.GeometryFiltrationThresholds | None)

• plot_thresholds (Union)

• plot_populations (Literal)

• mol (rdkit.Chem.rdchem.Mol | None)

• drop_empty_trajectories (bool)

Return type:

Union

calculate_bond_length_filtranda(geometry_thresholds=None, mol=None)

Wrapper for shnitsel.clean.filter_geo.calculate_bond_length_filtranda().

Parameters:

• geometry_thresholds (dict[str, float] | shnitsel.clean.filter_geo.GeometryFiltrationThresholds | None)

• mol (rdkit.Chem.rdchem.Mol | None)

Return type:

xarray.core.dataarray.DataArray

filter_by_length(filter_method='truncate', geometry_thresholds=None, mol=None, plot_thresholds=False, plot_populations=False)

Wrapper for shnitsel.clean.filter_geo.filter_by_length().

Parameters:

• filter_method (Union)

• geometry_thresholds (dict[str, float] | shnitsel.clean.filter_geo.GeometryFiltrationThresholds | None)

• mol (rdkit.Chem.rdchem.Mol | None)

• plot_thresholds (Union)

• plot_populations (Literal)

Return type:

Optional

omit()

Wrapper for shnitsel.clean.common.omit().

Return type:

Optional

truncate()

Wrapper for shnitsel.clean.common.truncate().

Return type:

Union

transect(cutoff_time)

Wrapper for shnitsel.clean.common.transect().

Parameters:

cutoff_time (float)

Return type:

shnitsel.data.dataset_containers.trajectory.Trajectory | None

write_ase_db(db_path, db_format=None, keys_to_write=None, preprocess=True, force=False)

Wrapper for shnitsel.io.ase.write.write_ase_db().

Parameters:

• db_path (str)

• db_format (Optional)

• keys_to_write (Optional)

• preprocess (bool)

• force (bool)

pls_ds(xname, yname, n_components=2, common_dim=None)

Wrapper for shnitsel.analyze.pls.pls_ds().

Parameters:

• xname (str)

• yname (str)

• n_components (int)

• common_dim (str | None)

Return type:

xarray.core.dataset.Dataset

hops_mask_from_active_state(hop_type_selection=None, dim=None)

Wrapper for shnitsel.analyze.hops.hops_mask_from_active_state().

Parameters:

• hop_type_selection (Union)

• dim (str | None)

Return type:

xarray.core.dataarray.DataArray | shnitsel.data.tree.node.TreeNode[DataArray]

filter_data_at_hops(hop_type_selection=None)

Wrapper for shnitsel.analyze.hops.filter_data_at_hops().

Parameters:

hop_type_selection (Union)

Return type:

shnitsel.data.dataset_containers.data_series.DataSeries | xarray.core.dataarray.DataArray | shnitsel.data.tree.node.TreeNode[DataSeries] | shnitsel.data.tree.node.TreeNode[DataArray]

focus_hops(hop_types=None, window=None)

Wrapper for shnitsel.analyze.hops.focus_hops().

Parameters:

• hop_types (list[tuple[int, int]] | None)

• window (slice | None)

assign_hop_time(hop_types=None, which='last')

Wrapper for shnitsel.analyze.hops.assign_hop_time().

Parameters:

• hop_types (list[tuple[int, int]] | None)

• which (Literal)

FrameSelector(data_var=None, dim=None, xname=None, yname=None, title='', allowed_ws_origin=None, webgl=True)

Wrapper for shnitsel.vis.plot.select.FrameSelector().

TrajSelector(data_var=None, dim=None, xname=None, yname=None, title='', allowed_ws_origin=None, webgl=True)

Wrapper for shnitsel.vis.plot.select.TrajSelector().